Variant report

Variant	rs6701037
Chromosome Location	chr1:175120079-175120080
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:175115119..175117020-chr1:175119706..175122509,2	K562	blood:
2	chr1:174999884..175001558-chr1:175119055..175120862,2	K562	blood:
3	chr1:175119497..175122069-chr1:175128749..175130315,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10489326	0.85[MEX][hapmap]
rs1057239	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[MEX][hapmap]
rs1057246	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs1057301	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1057302	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1057305	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912901	0.81[CEU][hapmap]
rs11580331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583687	0.81[CEU][hapmap];0.94[MEX][hapmap]
rs11585617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094153	0.80[ASW][hapmap]
rs12747817	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894709	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs2157588	0.93[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap]
rs2285219	0.85[CEU][hapmap]
rs2685	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs34370567	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs34493921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4650716	0.85[MEX][hapmap]
rs6425323	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6659824	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6677097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683533	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929	0.92[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7512413	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7514749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521981	0.80[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508648	chr1:175056387-175121913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alcohol dependence	21703634	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6701037	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL
rs6701037	SUSD1	trans	cerebellum	SCAN
rs6701037	KIAA0040	cis	multi-tissue	Pritchard
rs6701037	KIAA0040	cis	Lymphoblastoid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175110200-175127400	Weak transcription	Left Ventricle	heart
2	chr1:175111400-175122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:175115000-175125000	Weak transcription	Right Atrium	heart
4	chr1:175116400-175121200	Weak transcription	Placenta	Placenta
5	chr1:175116600-175121400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:175116800-175121000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:175119000-175120200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:175119000-175120200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:175119000-175120400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:175119000-175120400	Enhancers	Liver	Liver
11	chr1:175119000-175121400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:175119400-175120200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:175119400-175120400	Enhancers	HMEC	breast
14	chr1:175119400-175121200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:175119600-175120200	Enhancers	Osteobl	bone
16	chr1:175119600-175120400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
17	chr1:175119800-175120200	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:175120000-175120200	Enhancers	Stomach Smooth Muscle	stomach
19	chr1:175120000-175120200	Bivalent Enhancer	NHEK	skin
20	chr1:175120000-175120400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:175120000-175120600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:175120000-175121200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:175120000-175121400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon

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